What was your mm_pbsa.pl input file? Are temporary files (_MMPBSA_*) still
being written to for MMPBSA.py?
On Thu, Dec 15, 2011 at 11:21 AM, Qinghua Liao <fantasticqhl.gmail.com>wrote:
> Dear amber users,
>
> Is it very slow for calculating binding energy and decomposition
> simultaneously? It has been more than 24 hours for the calculation using 16
> cores' MMPBSA.MPI, and it has already finished using 8 core's
> mm_pbsa.plfor the calculation of binding energy. Here is the input
> file:
>
> &general
> startframe=1, endframe=400, interval=1,
> verbose=1, keep_files=1,
> /
> &gb
> igb=5, saltcon=0.10, surften=0.0072, surfoff=0.00,
> /
> &pb
> indi=1.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4,
> inp=1, istrng=0.10, cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4.0,
> /
> &decomp
> idecomp=2, dec_verbose=3,
> /
>
> I guess that there may be some problem with my input file, could someone
> give me a suggestion? Thanks very much!
>
> --
> Best Regards,
>
> Qinghua
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Dec 15 2011 - 11:00:03 PST
